A paper mill has recently proposed the treatment of methanol-containing condensate using anaerobic pretreatment system as an alternative control for hazardous air pollutants (HAPs) 40 CFR Part 63 Subpart S - Maximum Achievable Control Technology. To investigate the potential use of an anaerobic digester and to reduce methanol in wastewater treatment plants (WWTPs), the fate of methanol in a digester was examined. A series of laboratory-scale experiments were conducted and a mathematical model was developed to evaluate the fate of methanol during anaerobic treatment. From a mathematical model, the losses of methanol through the Styrofoam® cover system and volatilizations were calculated to be almost zero (<0.01%). Since acetaldehyde and methyl ethyl ketone have one order of Henry’s law constants magnitude smaller than methanol, the release of these by-products into the atmosphere is expected to be much smaller than methanol, which was found to have an almost zero loss through volatilization.